Align 3-isopropylmalate dehydratase small subunit 1; EC 4.2.1.33; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1 (uncharacterized)
to candidate BPHYT_RS30145 BPHYT_RS30145 aconitate hydratase
Query= curated2:Q8TX94 (170 letters) >FitnessBrowser__BFirm:BPHYT_RS30145 Length = 865 Score = 43.9 bits (102), Expect = 7e-09 Identities = 22/57 (38%), Positives = 34/57 (59%), Gaps = 1/57 (1%) Query: 56 VIVAGKNFGCGSSREHAPIALKAAGIACVVTRSFARIFYRNAINLG-LPLVVCPGVD 111 +++AG ++G GSSR+ A ++ AG +V F RI N + +G LPL PGV+ Sbjct: 735 IVIAGADYGQGSSRDWAAKGVRLAGAEAIVAEGFERIHRTNLVGMGVLPLEFKPGVN 791 Lambda K H 0.321 0.143 0.428 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 359 Number of extensions: 26 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 170 Length of database: 865 Length adjustment: 30 Effective length of query: 140 Effective length of database: 835 Effective search space: 116900 Effective search space used: 116900 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory